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<div class="title">SequenceFileReader.hpp</div>  </div>
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<a href="_sequence_file_reader_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a>&quot;</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160; </div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="preprocessor">#include &lt;cstdlib&gt;</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="preprocessor">#include &lt;cstdio&gt;</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160; </div>
<div class="line"><a name="l00008"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html">    8</a></span>&#160;<span class="keyword">class </span><a class="code" href="class_sequence_file_reader.html">SequenceFileReader</a> {</div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00010"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">   10</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> {</div>
<div class="line"><a name="l00011"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1">   11</a></span>&#160;        <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1">dna</a>, <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41">amino</a>, <span class="keyword">null</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7a9388aafb7eda9f884eed4c4dc315cc24">   12</a></span>&#160;    };</div>
<div class="line"><a name="l00013"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a4ed189180afd320f49605425fad1a0d9">   13</a></span>&#160;    std::string **<a class="code" href="class_sequence_file_reader.html#a4ed189180afd320f49605425fad1a0d9">seqs</a>;</div>
<div class="line"><a name="l00014"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#ac5ad200019599845c0f1bc226ce0161b">   14</a></span>&#160;    std::string **<a class="code" href="class_sequence_file_reader.html#ac5ad200019599845c0f1bc226ce0161b">names</a>;</div>
<div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a9318592fe459d2b67d3fb191b1f75057">   15</a></span>&#160;    <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> <a class="code" href="class_sequence_file_reader.html#a9318592fe459d2b67d3fb191b1f75057">alphType</a>;</div>
<div class="line"><a name="l00016"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#aac56176cc7a6ed92728a106576ec3382">   16</a></span>&#160;    <span class="keywordtype">int</span> <a class="code" href="class_sequence_file_reader.html#aac56176cc7a6ed92728a106576ec3382">numSeqs</a>;</div>
<div class="line"><a name="l00017"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">   17</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">fileType</a> {</div>
<div class="line"><a name="l00018"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2">   18</a></span>&#160;        <a class="code" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2">fasta</a>, <a class="code" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c">stockholm</a></div>
<div class="line"><a name="l00019"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c">   19</a></span>&#160;    };</div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160; </div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;    <a class="code" href="class_sequence_file_reader.html#afefc977e0ab5e10c56afbf0f2fa2ada8">SequenceFileReader</a>(std::string *filename, <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> alphTypeIn);</div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160; </div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;    <a class="code" href="class_sequence_file_reader.html#a68f93cafb0fff8017a6ddfdac763b2ec">~SequenceFileReader</a>();</div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160; </div>
<div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="class_sequence_file_reader.html#a5599fbffb34bd065bfb846947c6e9c41">   25</a></span>&#160;    <a class="code" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">fileType</a> <a class="code" href="class_sequence_file_reader.html#a5599fbffb34bd065bfb846947c6e9c41">filetype</a>;</div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160; </div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;    std::string **<a class="code" href="class_sequence_file_reader.html#ac6ddf2c86a6e8c25f21d9e1381cb08ce">getSeqs</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160; </div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;    std::string **<a class="code" href="class_sequence_file_reader.html#a90a7fe721e3311573775ab8f7c946ec9">getNames</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    <a class="code" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> <a class="code" href="class_sequence_file_reader.html#a19cd3893e28924779bfcb74a1cece03b">getAlphType</a>() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;};</div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160; </div>
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<div class="ttc" id="aclass_sequence_file_reader_html_a8cc42e15f26ed4a680ac4b968f0922a7"><div class="ttname"><a href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">SequenceFileReader::AlphabetType</a></div><div class="ttdeci">AlphabetType</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:10</div></div>
<div class="ttc" id="a_exception_handler_8hpp_html"><div class="ttname"><a href="_exception_handler_8hpp.html">ExceptionHandler.hpp</a></div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a4ed189180afd320f49605425fad1a0d9"><div class="ttname"><a href="class_sequence_file_reader.html#a4ed189180afd320f49605425fad1a0d9">SequenceFileReader::seqs</a></div><div class="ttdeci">std::string ** seqs</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:13</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a68f93cafb0fff8017a6ddfdac763b2ec"><div class="ttname"><a href="class_sequence_file_reader.html#a68f93cafb0fff8017a6ddfdac763b2ec">SequenceFileReader::~SequenceFileReader</a></div><div class="ttdeci">~SequenceFileReader()</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.cpp:157</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a5599fbffb34bd065bfb846947c6e9c41"><div class="ttname"><a href="class_sequence_file_reader.html#a5599fbffb34bd065bfb846947c6e9c41">SequenceFileReader::filetype</a></div><div class="ttdeci">fileType filetype</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:25</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2"><div class="ttname"><a href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2">SequenceFileReader::fasta</a></div><div class="ttdeci">@ fasta</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:18</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html"><div class="ttname"><a href="class_sequence_file_reader.html">SequenceFileReader</a></div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:8</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_ac6ddf2c86a6e8c25f21d9e1381cb08ce"><div class="ttname"><a href="class_sequence_file_reader.html#ac6ddf2c86a6e8c25f21d9e1381cb08ce">SequenceFileReader::getSeqs</a></div><div class="ttdeci">std::string ** getSeqs() const</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.cpp:173</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_aac56176cc7a6ed92728a106576ec3382"><div class="ttname"><a href="class_sequence_file_reader.html#aac56176cc7a6ed92728a106576ec3382">SequenceFileReader::numSeqs</a></div><div class="ttdeci">int numSeqs</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:16</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a19cd3893e28924779bfcb74a1cece03b"><div class="ttname"><a href="class_sequence_file_reader.html#a19cd3893e28924779bfcb74a1cece03b">SequenceFileReader::getAlphType</a></div><div class="ttdeci">AlphabetType getAlphType() const</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.cpp:181</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1"><div class="ttname"><a href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1">SequenceFileReader::dna</a></div><div class="ttdeci">@ dna</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:11</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c"><div class="ttname"><a href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c">SequenceFileReader::stockholm</a></div><div class="ttdeci">@ stockholm</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:18</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a38d7a5bd2e01b009daa2fa7f0909ed57"><div class="ttname"><a href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">SequenceFileReader::fileType</a></div><div class="ttdeci">fileType</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:17</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41"><div class="ttname"><a href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41">SequenceFileReader::amino</a></div><div class="ttdeci">@ amino</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:11</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a9318592fe459d2b67d3fb191b1f75057"><div class="ttname"><a href="class_sequence_file_reader.html#a9318592fe459d2b67d3fb191b1f75057">SequenceFileReader::alphType</a></div><div class="ttdeci">AlphabetType alphType</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:15</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_afefc977e0ab5e10c56afbf0f2fa2ada8"><div class="ttname"><a href="class_sequence_file_reader.html#afefc977e0ab5e10c56afbf0f2fa2ada8">SequenceFileReader::SequenceFileReader</a></div><div class="ttdeci">SequenceFileReader(std::string *filename, AlphabetType alphTypeIn)</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.cpp:5</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_ac5ad200019599845c0f1bc226ce0161b"><div class="ttname"><a href="class_sequence_file_reader.html#ac5ad200019599845c0f1bc226ce0161b">SequenceFileReader::names</a></div><div class="ttdeci">std::string ** names</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.hpp:14</div></div>
<div class="ttc" id="aclass_sequence_file_reader_html_a90a7fe721e3311573775ab8f7c946ec9"><div class="ttname"><a href="class_sequence_file_reader.html#a90a7fe721e3311573775ab8f7c946ec9">SequenceFileReader::getNames</a></div><div class="ttdeci">std::string ** getNames() const</div><div class="ttdef"><b>Definition:</b> SequenceFileReader.cpp:177</div></div>
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